Affinage

PEX6

Peroxisomal ATPase PEX6 · UniProt Q13608

Length
980 aa
Mass
104.1 kDa
Annotated
2026-04-29
47 papers in source corpus 15 papers cited in narrative 15 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PEX6 is a AAA+ ATPase that functions as an essential component of the peroxisomal matrix protein import machinery by powering the extraction and recycling of the cargo receptor PEX5 from the peroxisomal membrane. PEX6 forms an alternating heterohexameric double-ring complex with PEX1 in which the C-terminal D2 ring is catalytically active and processively threads monoubiquitinated PEX5 through its central pore via a staircase of pore-1 loops, globally unfolding the substrate during ATP-dependent extraction (PMID:29321502, PMID:37741838, PMID:29884772). The N1 domain of PEX6 mediates recruitment to the peroxisomal membrane through binding the tail-anchored tether PEX15 (yeast)/PEX26 (mammals) and simultaneously stabilizes the PEX1–PEX6 hexamer by contacting an extended loop from the PEX1 D2 domain (PMID:38036174, PMID:26170309). Loss of PEX6 function underlies peroxisome biogenesis disorders including Zellweger syndrome (complementation group C), and PEX6-dependent extraction of ubiquitinated PEX5 is coupled to dynamic topological remodeling of the PEX14 docking complex at the peroxisomal membrane (PMID:8940266, PMID:41581879).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 1996 High

    Identification of PEX6 as a cytoplasmic AAA ATPase essential for peroxisome biogenesis and PTS1-receptor stability established the molecular identity of the gene defective in Zellweger complementation group C.

    Evidence Functional complementation in Zellweger patient fibroblasts and CHO cells, ATPase domain K→R mutagenesis, Western blot for PEX5 stability

    PMID:8670792 PMID:8940266

    Open questions at the time
    • Whether PEX6 acts alone or requires a partner ATPase was unknown
    • The substrate of PEX6's ATPase activity was not identified
    • How PEX6 is recruited to peroxisomes was not determined
  2. 1998 High

    Demonstrating that PEX1 and PEX6 physically interact and that disease mutations weaken this interaction established the functional ATPase complex and explained genotype–phenotype relationships in peroxisome biogenesis disorders.

    Evidence Yeast two-hybrid, in vitro pulldown, allele-specific genetic suppression between PEX1 and PEX6

    PMID:9671729

    Open questions at the time
    • Stoichiometry and architecture of the PEX1–PEX6 complex were unknown
    • The direct substrate of the complex had not been identified
  3. 2002 High

    Showing that PEX6 converts import-incompetent peroxisomal ghost membranes into functional peroxisomes demonstrated that PEX6 acts downstream of membrane assembly to enable matrix protein translocation.

    Evidence EM and immunofluorescence of PEX6-deficient CHO cells before and after complementation, GFP-PTS1 reporter

    PMID:11854424

    Open questions at the time
    • The step at which PEX6 acts in the import cycle (receptor docking, translocation, or recycling) was not resolved
    • Whether PEX6 acts on PEX5 directly or indirectly was unclear
  4. 2011 High

    Identification of AWP1/ZFAND6 as a PEX6-binding cofactor that recognizes monoubiquitinated PEX5 and stimulates its export linked PEX6 function specifically to ubiquitin-dependent receptor recycling.

    Evidence Co-IP, in vitro PEX5 export assay, RNAi knockdown, antibody inhibition

    PMID:21980954

    Open questions at the time
    • Whether AWP1 is essential in vivo or merely enhances export efficiency was not resolved
    • The mechanism by which AWP1 cooperates with the PEX1–PEX6 ATPase was not determined
  5. 2014 Medium

    Demonstrating that loss of Pex1/Pex6/Pex15 triggers enhanced pexophagy via Atg36 revealed that the exportomer's activity protects peroxisomes from autophagic degradation, explaining the peroxisome-loss phenotype in mutant cells.

    Evidence Genetic epistasis with atg1Δ and atg36 mutants, fluorescence microscopy in S. cerevisiae

    PMID:24657987

    Open questions at the time
    • The pexophagy signal generated by exportomer deficiency was not molecularly defined
    • Whether this pexophagy mechanism is conserved in mammals was not tested
  6. 2015 High

    Cryo-EM structures revealed the unprecedented alternating PEX1–PEX6 heterohexameric double-ring architecture with a catalytically inactive D1 ring and an active asymmetric D2 ring, providing the structural framework for understanding substrate processing.

    Evidence Cryo-EM of the S. cerevisiae Pex1/Pex6 complex, computational domain fitting

    PMID:26170309

    Open questions at the time
    • No substrate was captured in the pore, so the translocation mechanism remained hypothetical
    • How the complex engages the peroxisomal membrane was not structurally resolved
  7. 2018 High

    Reconstituted translocase activity and cryo-EM of substrate-engaged complexes established that PEX1/PEX6 is a processive protein unfoldase that threads substrates through its D2 pore via pore-loop contacts, with monoubiquitinated PEX5 as its bona fide physiological substrate.

    Evidence In vitro unfolding/translocation assay with Pex15, cryo-EM of Pex1/Pex6–Pex15 complex, cell-free PEX5 export with photoaffinity cross-linking and PEGylation unfolding readout

    PMID:29321502 PMID:29884772

    Open questions at the time
    • The step-by-step nucleotide cycle driving translocation was not resolved
    • Whether PEX5 and PEX15 are threaded by the same or distinct mechanisms was unclear
  8. 2023 High

    High-resolution cryo-EM with endogenous substrate trapped in the pore revealed the twin-seam translocation mechanism and showed that the PEX6 N1 domain serves dual roles as membrane tether anchor and hexamer stabilizer, completing the structural model of the translocase.

    Evidence Cryo-EM with endogenous substrate trapping, X-ray crystallography of Pex6 N1, in vivo complementation of N1 deletion

    PMID:37741838 PMID:38036174

    Open questions at the time
    • The identity of the endogenous substrate trapped in the pore was not determined
    • Structural basis of how PEX26 (mammalian tether) engages PEX6 N1 awaits high-resolution data
    • How the twin-seam mechanism coordinates with ubiquitin recognition is not resolved
  9. 2026 Medium

    Demonstrating that PEX6 and PEX5 ubiquitination jointly drive reversible topological remodeling of the PEX14 docking complex established that receptor extraction is mechanistically coupled to structural reorganization of the translocation channel.

    Evidence Protease protection assay, immunofluorescence, pharmacological AAA+ inhibition (NEM), ubiquitin inhibitor MLN-7243, PEX6/PEX26 knockdown

    PMID:41581879

    Open questions at the time
    • Whether PEX14 remodeling is a cause or consequence of PEX5 extraction is not distinguished
    • The structural basis for PEX14 topology change at the membrane is unknown
    • Single study; independent confirmation is needed

Open questions

Synthesis pass · forward-looking unresolved questions
  • The precise nucleotide-driven conformational cycle that couples ATP hydrolysis in the D2 ring to stepwise substrate translocation, and how ubiquitin on PEX5 is recognized and processed during threading, remain structurally unresolved.
  • No time-resolved or single-molecule measurements of the translocation cycle exist
  • Structural basis of ubiquitin recognition by the PEX1–PEX6 pore is unknown
  • Role of the catalytically inactive D1 ring in allosteric regulation of translocation is not mechanistically defined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140657 ATP-dependent activity 5 GO:0016787 hydrolase activity 3 GO:0044183 protein folding chaperone 3
Localization
GO:0005777 peroxisome 2 GO:0005829 cytosol 1 GO:0005929 cilium 1
Pathway
R-HSA-1852241 Organelle biogenesis and maintenance 5 R-HSA-9609507 Protein localization 3 R-HSA-9612973 Autophagy 1
Partners
AWP1PEX1PEX14PEX15PEX26PEX5
Complex memberships
PEX1–PEX6 heterohexamer

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1996 PEX6 (PXAAA1/PAF-2) encodes a cytoplasmic AAA-family ATPase required for peroxisomal protein import; substitution of the conserved lysine in the ATPase domain abolishes biological activity, and PEX6 is required for stability of the PTS1 receptor (Pxr1p/PEX5). Functional complementation in patient fibroblasts, ATPase domain mutagenesis (K→R), Western blot for PTS1 receptor stability The EMBO journal High 8670792
1996 Human PEX6 (PAF-2) restores peroxisome assembly in fibroblasts from complementation group C Zellweger patients, confirming its essential role in peroxisome biogenesis. Functional complementation by cDNA transfection in patient-derived CHO and Zellweger fibroblasts American journal of human genetics High 8940266
1998 PEX1 and PEX6 physically interact to form a complex essential for peroxisome biogenesis; overexpression of one suppresses loss-of-function alleles of the other in an allele-specific manner; the PEX1 G843D disease mutation attenuates the PEX1–PEX6 interaction. Yeast two-hybrid assay, in vitro binding (pulldown), allele-specific genetic suppression Proceedings of the National Academy of Sciences of the United States of America High 9671729
2002 In PEX6-deficient CHO cells, peroxisomal ghosts are complex double-membraned structures; upon complementation with PEX6 cDNA, these structures become import-competent and are converted into functional peroxisomes, establishing PEX6's role in enabling matrix protein import into pre-existing membrane structures. Genetic complementation, immunofluorescence microscopy, electron microscopy, GFP-PTS1 reporter, biochemical fractionation Molecular biology of the cell High 11854424
2011 AWP1/ZFAND6 interacts with PEX6 AAA ATPase (but not with PEX1–PEX6 complexes) and preferentially binds cysteine-monoubiquitinated PEX5 via its A20 zinc-finger domain; AWP1 stimulates PEX5 export from peroxisomes and is required for PTS1-protein import. In vitro Pex5 export assay, Co-IP, antibody inhibition, RNAi knockdown, PEX5 stability assay Traffic (Copenhagen, Denmark) High 21980954
2015 Cryo-EM structures of the Pex1/Pex6 complex reveal an unprecedented heterohexameric double ring in which Pex1 and Pex6 alternate; the N-terminal D1 ring is catalytically inactive and symmetric, while the C-terminal D2 ring is active and asymmetric; the N1 domain of Pex1 is mobile, suggesting coordinated subunit activity analogous to p97/NSF. Cryo-electron microscopy, computational domain fitting, Monte Carlo modeling with energy minimization Proceedings of the National Academy of Sciences of the United States of America High 26170309
2018 The yeast Pex1/Pex6 complex is a protein translocase that unfolds its substrate Pex15 by processive threading through the central pore in a pore-loop-dependent and ATP-hydrolysis-dependent manner; Pex15 binds the N-terminal domains of Pex6 before its disordered C-terminal region engages the pore loops; Pex15 also directly binds the cargo receptor Pex5, linking Pex1/Pex6 to the import machinery. In vitro unfolding/translocation assay, cryo-EM of Pex1/Pex6–Pex15 complex, pulldown/binding assays, ATPase mutagenesis Nature communications High 29321502
2018 DTM-embedded monoubiquitinated PEX5 (Ub-PEX5) interacts directly with both PEX1 and PEX6 through its ubiquitin moiety, and the PEX5 polypeptide chain is globally unfolded during ATP-dependent extraction, establishing monoubiquitinated PEX5 as a bona fide substrate of the PEX1–PEX6 complex. Cell-free in vitro Pex5 export system, photoaffinity cross-linking, protein PEGylation assay The Journal of biological chemistry High 29884772
2023 CryoEM structures of S. cerevisiae Pex1/Pex6 with an endogenous substrate trapped in the D2 pore reveal that pairs of Pex1/Pex6 D2 subdomains engage substrate via a staircase of pore-1 loops; the inactive D1 ring undergoes ATP-hydrolysis-driven conformational changes; a 'twin-seam' Pex1/Pex6(D2) heterodimer disengages from the staircase to drive substrate translocation. Cryo-EM with endogenous substrate trapping, structural analysis of pore-loop contacts Nature communications High 37741838
2023 The N1 domain of Pex6 mediates binding to the peroxisomal membrane tether Pex15 and to an extended loop from the D2 ATPase domain of Pex1 that stabilizes the Pex1/Pex6 heterohexamer; deletion of Pex6 N1 abolishes in vivo peroxisome function despite retaining ATPase activity in vitro. X-ray crystallography of isolated Pex6 N1 domain, cryo-EM of Pex1/Pex6, AlphaFold2 modeling, biochemical pulldown assays, in vivo complementation The Journal of biological chemistry High 38036174
2014 In S. cerevisiae, deficiency of the exportomer subunits Pex1, Pex6, and Pex15 causes enhanced pexophagy via the Atg36 receptor and Atg11 scaffold; accumulation of ubiquitinated peroxin receptors at the peroxisomal membrane does not, by itself, trigger pexophagy in yeast, as shown by genetic epistasis. Genetic deletion analysis (pex1Δ, atg1Δ, atg36 mutants), fluorescence microscopy of phagophore assembly sites, epistasis analysis Autophagy Medium 24657987
2015 PEX6 localizes to cilia of retinal photoreceptor cells and to the apical extensions of secretory ameloblasts and odontoblasts in mice, linking peroxisome biogenesis to photoreceptor ciliary function. Immunofluorescence microscopy in mouse tissues (retina, ameloblasts, odontoblasts) Human mutation Medium 26593283
2007 In S. cerevisiae, extra copies of PEX6 suppress mitochondrial aging defects in an atp2 mutant by improving import kinetics of Atp2p into mitochondria, restoring normal mitochondrial inheritance; this function requires ATP binding and/or hydrolysis activity of Pex6p. Multicopy suppressor screen, mitochondrial protein import assay, ATPase mutant analysis, daughter-cell mitochondrial inheritance assay Aging cell Medium 17465979
2026 Pex6 (together with ubiquitination of Pex5) regulates reversible ATP-dependent topological remodeling of the Pex14 N-terminal domain at the peroxisomal membrane: normally the Pex14 N terminus faces the lumen, but loss of Pex6 or Pex26, or inhibition of AAA+ ATPases, exposes it to the cytoplasm; blocking ubiquitin activation prevents this reorientation, linking Pex5 ubiquitination and Pex6-mediated extraction to structural reorganization of the docking–translocation complex. Immunofluorescence microscopy, protease protection assay, pharmacological inhibition of AAA+ ATPases (NEM), ubiquitin inhibitor (MLN-7243), Pex6/Pex26 knockdown/knockout The Journal of biological chemistry Medium 41581879
2003 In Hansenula polymorpha, a point mutation in the first AAA module of Pex6p (G737E) combined with a secondary mutation in the second AAA domain (R1000G) creates a cold-sensitive conditional allele, demonstrating that both AAA cassettes contribute functionally to peroxisome biogenesis. UV mutagenesis, intragenic suppressor analysis, sequencing, electron microscopy of peroxisomes FEMS yeast research Low 14613878

Source papers

Stage 0 corpus · 47 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1996 The peroxisome biogenesis disorder group 4 gene, PXAAA1, encodes a cytoplasmic ATPase required for stability of the PTS1 receptor. The EMBO journal 165 8670792
1998 Disruption of a PEX1-PEX6 interaction is the most common cause of the neurologic disorders Zellweger syndrome, neonatal adrenoleukodystrophy, and infantile Refsum disease. Proceedings of the National Academy of Sciences of the United States of America 105 9671729
1996 Human peroxisome assembly factor-2 (PAF-2): a gene responsible for group C peroxisome biogenesis disorder in humans. American journal of human genetics 96 8940266
2011 Arabidopsis ABERRANT PEROXISOME MORPHOLOGY9 is a peroxin that recruits the PEX1-PEX6 complex to peroxisomes. The Plant cell 73 21487094
2015 Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy. Proceedings of the National Academy of Sciences of the United States of America 68 26170309
2002 A PEX6-defective peroxisomal biogenesis disorder with severe phenotype in an infant, versus mild phenotype resembling Usher syndrome in the affected parents. American journal of human genetics 59 11873320
2014 Deficiency of the exportomer components Pex1, Pex6, and Pex15 causes enhanced pexophagy in Saccharomyces cerevisiae. Autophagy 57 24657987
2018 The peroxisomal AAA-ATPase Pex1/Pex6 unfolds substrates by processive threading. Nature communications 52 29321502
2007 Jasmonate biosynthesis in Arabidopsis thaliana requires peroxisomal beta-oxidation enzymes--additional proof by properties of pex6 and aim1. Phytochemistry 47 17544464
2011 AWP1/ZFAND6 functions in Pex5 export by interacting with cys-monoubiquitinated Pex5 and Pex6 AAA ATPase. Traffic (Copenhagen, Denmark) 46 21980954
2017 Allelic Expression Imbalance Promoting a Mutant PEX6 Allele Causes Zellweger Spectrum Disorder. American journal of human genetics 41 29220678
2018 Peroxisomal monoubiquitinated PEX5 interacts with the AAA ATPases PEX1 and PEX6 and is unfolded during its dislocation into the cytosol. The Journal of biological chemistry 39 29884772
2006 Identification of novel mutations in PEX2, PEX6, PEX10, PEX12, and PEX13 in Zellweger spectrum patients. Human mutation 39 17041890
2005 Identification and characterization of three peroxins--PEX6, PEX10 and PEX12--involved in glycosome biogenesis in Trypanosoma brucei. Biochimica et biophysica acta 37 16388862
2015 PEX6 is Expressed in Photoreceptor Cilia and Mutated in Deafblindness with Enamel Dysplasia and Microcephaly. Human mutation 34 26593283
2012 A founder mutation in the PEX6 gene is responsible for increased incidence of Zellweger syndrome in a French Canadian population. BMC medical genetics 32 22894767
2010 Spectrum of PEX6 mutations in Zellweger syndrome spectrum patients. Human mutation 32 19877282
1999 Genomic structure and identification of 11 novel mutations of the PEX6 (peroxisome assembly factor-2) gene in patients with peroxisome biogenesis disorders. Human mutation 25 10408779
2007 A novel role of peroxin PEX6: suppression of aging defects in mitochondria. Aging cell 24 17465979
2017 miRNA-Related Polymorphisms in miR-423 (rs6505162) and PEX6 (rs1129186) and Risk of Esophageal Squamous Cell Carcinoma in an Iranian Cohort. Genetic testing and molecular biomarkers 23 28430524
2002 Peroxisomes are formed from complex membrane structures in PEX6-deficient CHO cells upon genetic complementation. Molecular biology of the cell 23 11854424
2019 Structural Mapping of Missense Mutations in the Pex1/Pex6 Complex. International journal of molecular sciences 20 31374812
2000 Temperature-sensitive mutation of PEX6 in peroxisome biogenesis disorders in complementation group C (CG-C): comparative study of PEX6 and PEX1. Pediatric research 19 11004248
2018 A pex1 missense mutation improves peroxisome function in a subset of Arabidopsis pex6 mutants without restoring PEX5 recycling. Proceedings of the National Academy of Sciences of the United States of America 17 29555730
2017 The PEX1 ATPase Stabilizes PEX6 and Plays Essential Roles in Peroxisome Biology. Plant physiology 17 28600347
2014 Late-onset Zellweger spectrum disorder caused by PEX6 mutations mimicking X-linked adrenoleukodystrophy. Pediatric neurology 17 25079577
2017 Disparate peroxisome-related defects in Arabidopsis pex6 and pex26 mutants link peroxisomal retrotranslocation and oil body utilization. The Plant journal : for cell and molecular biology 16 28742939
2023 Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate. Nature communications 15 37741838
2018 Ophthalmic manifestations of Heimler syndrome due to PEX6 mutations. Ophthalmic genetics 15 29676688
2017 Mild Zellweger syndrome due to a novel PEX6 mutation: correlation between clinical phenotype and in silico prediction of variant pathogenicity. Journal of applied genetics 13 29047053
2019 A Mechanistic Perspective on PEX1 and PEX6, Two AAA+ Proteins of the Peroxisomal Protein Import Machinery. International journal of molecular sciences 12 31652724
2021 PEX6 Mutations in Peroxisomal Biogenesis Disorders: An Usher Syndrome Mimic. Ophthalmology science 8 36249295
2020 Exome sequencing identifies PEX6 mutations in three cases diagnosed with Retinitis Pigmentosa and hearing impairment. Molecular vision 8 32214787
2019 Two novel mutations of PEX6 in one Chinese Zellweger spectrum disorder and their clinical characteristics. Annals of translational medicine 7 31555682
2021 RNAi-mediated silencing of PEX6 and GAS1 genes of Fusarium oxysporum f. sp. lycopersici confers resistance against Fusarium wilt in tomato. 3 Biotech 6 34631344
2023 The N1 domain of the peroxisomal AAA-ATPase Pex6 is required for Pex15 binding and proper assembly with Pex1. The Journal of biological chemistry 5 38036174
2001 Identification and characterisation of PEX6 orthologues from plants. Biochimica et biophysica acta 5 11389979
2023 PEX6 Mutation in a Child with Infantile Refsum Disease-A Case Report and Literature Review. Children (Basel, Switzerland) 3 36980088
2016 Strong cis-acting expression quantitative trait loci for the genes encoding SNHG5 and PEX6. Medicine 3 28033303
2024 A novel splice variant in intron 10 of PEX6 is associated with Zellweger Syndrome in a Chinese neonate. Gene 1 39013483
2023 Zellweger's Syndrome With PEX6 Gene Mutation in Mixteco Neonates Due to Possible Founder Effect. Cureus 1 37842507
2003 Identification of intragenic mutations in the Hansenula polymorpha PEX6 gene that affect peroxisome biogenesis and methylotrophic growth. FEMS yeast research 1 14613878
2026 Pex6 and ubiquitination regulate topological remodeling of the peroxisomal membrane protein Pex14. The Journal of biological chemistry 0 41581879
2026 Unraveling PEX6: insights into very-long-chain fatty acid levels and peroxisome biogenesis disorders in pediatric populations. Annals of pediatric endocrinology & metabolism 0 41787707
2024 [Zellweger syndrome caused by PEX6 gene variation in 2 cases and literature review]. Zhonghua er ke za zhi = Chinese journal of pediatrics 0 38154976
2023 Purification of a Recombinant Human PEX1/PEX6 AAA+ ATPase Complex from HEK293TT Cells. Methods in molecular biology (Clifton, N.J.) 0 36952198
2023 The Pex6 N1 domain is required for Pex15 binding and proper assembly with Pex1. bioRxiv : the preprint server for biology 0 37745580